# This file is the result of combining several RDB files, specifically # T0286.t06.dssp-ebghstl.rdb (weight 1.53986) # T0286.t06.stride-ebghtl.rdb (weight 1.24869) # T0286.t06.str2.rdb (weight 1.54758) # T0286.t06.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0286.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0286.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1642 # # ============================================ # Comments from T0286.t06.stride-ebghtl.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0286.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1642 # # ============================================ # Comments from T0286.t06.str2.rdb # ============================================ # TARGET T0286 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0286.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1642 # # ============================================ # Comments from T0286.t06.alpha.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0286.t06-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1642 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0692 0.0348 0.8960 2 A 0.0610 0.0757 0.8633 3 S 0.0519 0.1775 0.7706 4 K 0.0683 0.1054 0.8263 5 T 0.2028 0.0291 0.7681 6 I 0.5167 0.0099 0.4735 7 K 0.8800 0.0042 0.1158 8 I 0.9260 0.0034 0.0706 9 M 0.9253 0.0037 0.0711 10 P 0.9033 0.0042 0.0925 11 V 0.7293 0.0353 0.2355 12 G 0.3412 0.0288 0.6300 13 D 0.1906 0.0770 0.7324 14 S 0.1966 0.1781 0.6253 15 C 0.1599 0.3313 0.5088 16 T 0.1819 0.3125 0.5056 17 E 0.1447 0.2645 0.5908 18 G 0.1175 0.1510 0.7315 19 M 0.1119 0.1289 0.7592 20 G 0.1059 0.0957 0.7984 21 G 0.0865 0.1435 0.7700 22 G 0.0714 0.1795 0.7490 23 E 0.0628 0.2205 0.7167 24 M 0.0499 0.2337 0.7164 25 G 0.0393 0.2163 0.7445 26 S 0.0573 0.3056 0.6371 27 Y 0.0554 0.6191 0.3256 28 R 0.0226 0.8052 0.1722 29 T 0.0064 0.9293 0.0642 30 E 0.0059 0.9329 0.0612 31 L 0.0050 0.9481 0.0469 32 Y 0.0047 0.9547 0.0406 33 R 0.0047 0.9585 0.0368 34 L 0.0048 0.9560 0.0393 35 L 0.0048 0.9461 0.0491 36 T 0.0058 0.9212 0.0730 37 Q 0.0083 0.8334 0.1584 38 A 0.0445 0.4631 0.4924 39 G 0.0416 0.0686 0.8897 40 L 0.0871 0.0410 0.8719 41 S 0.2423 0.0415 0.7162 42 I 0.5802 0.0216 0.3982 43 D 0.7711 0.0159 0.2131 44 F 0.8603 0.0163 0.1234 45 V 0.7134 0.0405 0.2461 46 G 0.4359 0.0392 0.5248 47 S 0.2811 0.0576 0.6613 48 Q 0.3078 0.0831 0.6092 49 R 0.2273 0.0948 0.6779 50 S 0.1571 0.0835 0.7594 51 G 0.1196 0.0739 0.8065 52 P 0.1349 0.1479 0.7172 53 S 0.1801 0.1516 0.6682 54 S 0.1840 0.1086 0.7074 55 L 0.1150 0.0545 0.8306 56 P 0.0958 0.0868 0.8175 57 D 0.0982 0.0902 0.8116 58 K 0.1182 0.1023 0.7796 59 D 0.1647 0.1254 0.7099 60 H 0.2397 0.1259 0.6344 61 E 0.2462 0.1313 0.6224 62 G 0.2796 0.0973 0.6231 63 H 0.2914 0.0852 0.6234 64 S 0.1836 0.0973 0.7191 65 G 0.1022 0.1079 0.7900 66 W 0.1501 0.1186 0.7313 67 T 0.1794 0.1404 0.6802 68 I 0.0576 0.5993 0.3430 69 P 0.0113 0.8447 0.1440 70 Q 0.0124 0.8509 0.1366 71 I 0.0118 0.8843 0.1039 72 A 0.0084 0.8697 0.1219 73 S 0.0060 0.8074 0.1866 74 N 0.0092 0.7632 0.2276 75 I 0.0092 0.8291 0.1617 76 N 0.0055 0.9111 0.0833 77 N 0.0052 0.9210 0.0738 78 W 0.0067 0.9230 0.0702 79 L 0.0074 0.8984 0.0942 80 N 0.0078 0.8276 0.1646 81 T 0.0118 0.6564 0.3318 82 H 0.0516 0.4016 0.5469 83 N 0.0808 0.0272 0.8920 84 P 0.0771 0.0562 0.8667 85 D 0.1246 0.0712 0.8042 86 V 0.8864 0.0049 0.1087 87 V 0.9310 0.0032 0.0658 88 F 0.9336 0.0031 0.0632 89 L 0.9263 0.0036 0.0701 90 W 0.8933 0.0038 0.1029 91 I 0.6360 0.0262 0.3378 92 G 0.3316 0.0298 0.6386 93 G 0.2149 0.0519 0.7332 94 N 0.1173 0.0732 0.8095 95 D 0.0920 0.1049 0.8030 96 L 0.0328 0.2013 0.7659 97 L 0.0601 0.1661 0.7738 98 L 0.1125 0.1028 0.7847 99 N 0.0762 0.0923 0.8315 100 G 0.0118 0.8304 0.1579 101 N 0.0109 0.8865 0.1025 102 L 0.0102 0.8973 0.0925 103 N 0.0129 0.8956 0.0915 104 A 0.0088 0.9007 0.0905 105 T 0.0082 0.8369 0.1550 106 G 0.0102 0.7978 0.1921 107 L 0.0048 0.9490 0.0462 108 S 0.0047 0.9600 0.0353 109 N 0.0047 0.9600 0.0353 110 L 0.0047 0.9605 0.0348 111 I 0.0047 0.9608 0.0345 112 D 0.0046 0.9609 0.0344 113 Q 0.0048 0.9571 0.0382 114 I 0.0049 0.9447 0.0504 115 F 0.0056 0.9132 0.0812 116 T 0.0079 0.7756 0.2165 117 V 0.0285 0.5688 0.4027 118 K 0.0819 0.0572 0.8609 119 P 0.0122 0.1546 0.8332 120 N 0.0229 0.0704 0.9067 121 V 0.2440 0.0164 0.7396 122 T 0.7347 0.0044 0.2608 123 L 0.9302 0.0032 0.0666 124 F 0.9303 0.0034 0.0663 125 V 0.9258 0.0034 0.0708 126 A 0.8234 0.0120 0.1646 127 D 0.4776 0.0127 0.5097 128 Y 0.2053 0.0404 0.7543 129 Y 0.1303 0.0509 0.8188 130 P 0.0999 0.0565 0.8437 131 W 0.0554 0.0413 0.9033 132 P 0.0310 0.4300 0.5390 133 E 0.0135 0.6747 0.3117 134 A 0.0203 0.7101 0.2696 135 I 0.0113 0.8587 0.1300 136 K 0.0063 0.9084 0.0853 137 Q 0.0056 0.9184 0.0760 138 Y 0.0060 0.9207 0.0733 139 N 0.0078 0.9043 0.0879 140 A 0.0063 0.8754 0.1183 141 V 0.0083 0.8569 0.1349 142 I 0.0071 0.9192 0.0737 143 P 0.0053 0.9502 0.0445 144 G 0.0047 0.9590 0.0363 145 I 0.0047 0.9593 0.0360 146 V 0.0047 0.9591 0.0362 147 Q 0.0047 0.9597 0.0356 148 Q 0.0047 0.9589 0.0364 149 K 0.0049 0.9538 0.0413 150 A 0.0062 0.9331 0.0607 151 N 0.0072 0.8412 0.1516 152 A 0.0292 0.5036 0.4672 153 G 0.0455 0.1022 0.8523 154 K 0.0421 0.0669 0.8909 155 K 0.1227 0.0494 0.8278 156 V 0.5011 0.0139 0.4850 157 Y 0.8538 0.0043 0.1418 158 F 0.9171 0.0034 0.0795 159 V 0.8783 0.0056 0.1161 160 K 0.7371 0.0048 0.2581 161 L 0.2140 0.2238 0.5622 162 S 0.1007 0.3794 0.5200 163 E 0.0603 0.5628 0.3768 164 I 0.1103 0.5200 0.3696 165 Q 0.1477 0.4248 0.4275 166 F 0.1532 0.3402 0.5066 167 D 0.1241 0.1970 0.6789 168 R 0.0755 0.2174 0.7071 169 N 0.0724 0.1460 0.7816 170 T 0.0805 0.1242 0.7953 171 D 0.1403 0.1019 0.7578 172 I 0.2618 0.0936 0.6446 173 S 0.2293 0.0817 0.6891 174 W 0.1973 0.1361 0.6666 175 D 0.1423 0.1063 0.7515 176 G 0.1624 0.1016 0.7360 177 L 0.3126 0.0701 0.6173 178 H 0.3479 0.0665 0.5856 179 L 0.1314 0.1425 0.7261 180 S 0.0676 0.1147 0.8178 181 E 0.0053 0.9040 0.0907 182 I 0.0047 0.9397 0.0555 183 G 0.0047 0.9522 0.0431 184 Y 0.0047 0.9593 0.0360 185 K 0.0046 0.9609 0.0344 186 K 0.0047 0.9601 0.0352 187 I 0.0047 0.9592 0.0361 188 A 0.0047 0.9594 0.0359 189 N 0.0047 0.9585 0.0368 190 I 0.0048 0.9527 0.0425 191 W 0.0049 0.9495 0.0457 192 Y 0.0047 0.9556 0.0397 193 K 0.0047 0.9538 0.0415 194 Y 0.0049 0.9429 0.0522 195 T 0.0050 0.9338 0.0612 196 I 0.0050 0.9428 0.0522 197 D 0.0050 0.9430 0.0520 198 I 0.0055 0.9272 0.0673 199 L 0.0105 0.8866 0.1029 200 R 0.0102 0.8755 0.1143 201 A 0.0129 0.8643 0.1227 202 L 0.0251 0.7450 0.2300 203 A 0.0420 0.4225 0.5355 204 G 0.0401 0.1139 0.8460 205 E 0.0462 0.0701 0.8838